I am using the pivot_wider command to reshape my data, and I noticed all variables in my data set ( more than 100 columns) changed to "list" data type. They were integers, doubles and characters before I applied the pivot. Does anyone know how to prevent or resolve this?
This usually happens when you have more than one value per column and row identifier, if you don't pass a summarizing function you get a list with all values.
If you need more specific help, please provide a proper REPRoducible EXample (reprex) illustrating your issue.
library(tidyverse)
data.frame(
stringsAsFactors = FALSE,
KEY_PATIENT = c("uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[1]",
"uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[2]",
"uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[3]",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d/NumbVisitRepeat[1]",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d/NumbVisitRepeat[2]",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[1]",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[2]",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[3]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[1]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[2]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[3]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[4]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[5]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[6]",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[7]"),
KEY_visitNumber = c(1, 2, 3, 1, 2, 1, 2, 3, 1, 2, 3, 4, 5, 6, 7),
VisitDate = c("30/04/2019","6/10/2019",
"1/12/2019","15/11/2019","28/11/2019","24/01/2019",
"1/2/2019","8/2/2019","12/1/2019","10/2/2019","23/03/2019",
"15/05/2019","15/06/2019","27/07/2019","3/8/2019"),
HealthInsurYN = c("no","yes","yes","no","no",
"no","no","no","yes","yes","no","no","yes","yes",
"yes"),
BPMeasureYN = c("yes","yes","yes","yes",
"yes","yes","yes","yes","yes","yes","yes","yes",
"yes","yes","yes"),
SBP = c(150,147,137,180,160,180,
146,130,130,150,150,150,130,160,140),
BMIDocYN = c("no","no","no","no","no",
"no","no","no","no","no","no","no","no","no","no"),
AbdCirmDocYN = c("no","no","no","no","no",
"no","no","no","no","no","no","no","no","no","no"),
KEY_PARENT = c("uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0","uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0",
"uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0","uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a","uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a")
)
#> KEY_PATIENT KEY_visitNumber
#> 1 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[1] 1
#> 2 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[2] 2
#> 3 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0/NumbVisitRepeat[3] 3
#> 4 uuid:0047aac7-f803-4b76-beea-9f84cf81506d/NumbVisitRepeat[1] 1
#> 5 uuid:0047aac7-f803-4b76-beea-9f84cf81506d/NumbVisitRepeat[2] 2
#> 6 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[1] 1
#> 7 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[2] 2
#> 8 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0/NumbVisitRepeat[3] 3
#> 9 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[1] 1
#> 10 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[2] 2
#> 11 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[3] 3
#> 12 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[4] 4
#> 13 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[5] 5
#> 14 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[6] 6
#> 15 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a/NumbVisitRepeat[7] 7
#> VisitDate HealthInsurYN BPMeasureYN SBP BMIDocYN AbdCirmDocYN
#> 1 30/04/2019 no yes 150 no no
#> 2 6/10/2019 yes yes 147 no no
#> 3 1/12/2019 yes yes 137 no no
#> 4 15/11/2019 no yes 180 no no
#> 5 28/11/2019 no yes 160 no no
#> 6 24/01/2019 no yes 180 no no
#> 7 1/2/2019 no yes 146 no no
#> 8 8/2/2019 no yes 130 no no
#> 9 12/1/2019 yes yes 130 no no
#> 10 10/2/2019 yes yes 150 no no
#> 11 23/03/2019 no yes 150 no no
#> 12 15/05/2019 no yes 150 no no
#> 13 15/06/2019 yes yes 130 no no
#> 14 27/07/2019 yes yes 160 no no
#> 15 3/8/2019 yes yes 140 no no
#> KEY_PARENT
#> 1 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0
#> 2 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0
#> 3 uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0
#> 4 uuid:0047aac7-f803-4b76-beea-9f84cf81506d
#> 5 uuid:0047aac7-f803-4b76-beea-9f84cf81506d
#> 6 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0
#> 7 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0
#> 8 uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0
#> 9 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 10 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 11 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 12 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 13 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 14 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
#> 15 uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a
cli_visits_wider <- cli_visits%>%
arrange(KEY_visitNumber) %>% #
pivot_wider(
id_cols = KEY_PARENT,
names_from = KEY_visitNumber,
names_glue = "visit-{KEY_visitNumber}-{.value}",
values_from = VisitDate:AbdCirmDocYN)
#> Error in eval(lhs, parent, parent): object 'cli_visits' not found
Created on 2021-03-14 by the reprex package (v1.0.0)
Thank you andresrcs, here is a reprex above
Your example does not show any list type variables in the output.
p.s. this is after accounting for the need to assign the data.frame you shared with the cli_visits name
library(tidyverse)
cli_visit <- data.frame(
stringsAsFactors = FALSE,
VisitDate = c("30/04/2019","6/10/2019",
"1/12/2019","15/11/2019","28/11/2019","24/01/2019",
"1/2/2019","8/2/2019","12/1/2019","10/2/2019","23/03/2019",
"15/05/2019","15/06/2019","27/07/2019","3/8/2019",
"24/08/2019","19/10/2019","17/09/2019","15/10/2019",
"29/07/2019","31/07/2019","14/08/2019","10/8/2019",
"14/08/2019","8/2/2019"),
HealthInsurYN = c("no","yes","yes","no","no",
"no","no","no","yes","yes","no","no","yes","yes",
"yes","yes","yes","no","no","no","no","no","no",
"no","no"),
BPMeasureYN = c("yes","yes","yes","yes",
"yes","yes","yes","yes","yes","yes","yes","yes",
"yes","yes","yes","yes","yes","yes","yes","yes","yes",
"yes","yes","no","yes"),
WeightValue = c(NA,NA,NA,NA,NA,77,76,
75.5,98.4,97.5,99.2,99.5,99,98.3,98,97.8,98.6,95,
93,95,95,NA,NA,NA,60),
WeightUnit = c(NA,NA,NA,NA,NA,"kg","kg",
"kg","kg","kg","kg","kg","kg","kg","kg","kg",
"kg","kg","kg","kg","kg",NA,NA,NA,"kg"),
HeightDocYN = c("no","no","no","no","no",
"no","no","no","no","no","no","no","no","no","no",
"no","no","no","no","no","no","no","no","no",
"no"),
HeightUnit = c(NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA),
SBP = c(150,147,137,180,160,180,
146,130,130,150,150,150,130,160,140,130,150,160,
144,140,178,149,170,NA,151),
BMIDocYN = c("no","no","no","no","no",
"no","no","no","no","no","no","no","no","no","no",
"no","no","no","no","no","no","no","no","no",
"no"),
AbdCirmDocYN = c("no","no","no","no","no",
"no","no","no","no","no","no","no","no","no","no",
"no","no","no","no","no","no","no","no","no",
"no"),
KEY_PARENT = c("uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0","uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0",
"uuid:00226e78-ab5f-4c0b-b0a3-6b745e3fbca0",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d",
"uuid:0047aac7-f803-4b76-beea-9f84cf81506d",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0","uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0",
"uuid:0062433f-3e12-41dc-a13e-e63e121fe4a0",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a","uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a","uuid:0063cbfc-ce81-4b2a-b3b9-8d3bd8162a8a",
"uuid:0088b9f6-6305-4a87-bccb-2b2b66f91079",
"uuid:0088b9f6-6305-4a87-bccb-2b2b66f91079",
"uuid:00948da0-b3ca-4829-9f96-14f337c88b15","uuid:00948da0-b3ca-4829-9f96-14f337c88b15",
"uuid:00948da0-b3ca-4829-9f96-14f337c88b15",
"uuid:00b1510b-77be-4aff-b820-58614278e035",
"uuid:00b1510b-77be-4aff-b820-58614278e035",
"uuid:00b7756b-b6f1-4bc1-8a64-fd8c367c417b")
)
cli_visits_wider <- cli_visits%>%
arrange(KEY_visitNumber) %>% #
pivot_wider(
id_cols = KEY_PARENT,
names_from = KEY_visitNumber,
names_glue = "visit-{KEY_visitNumber}-{.value}",
values_from = VisitDate:AbdCirmDocYN)
#> Error in eval(lhs, parent, parent): object 'cli_visits' not found
Created on 2021-03-14 by the reprex package (v1.0.0)
I apologize. I was trying to provide as small a data sample as possible. This updated reprex shows the list error
Your new sample data contains no KEY_visitNumber column thus your code doesn't run. Can you check on that and make sure your code is reproducible before you post?
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